- 1
Setup
- 2 Load dataset and samples
- 3 miRNA, sponge 1 and target
genes
- 4 miRNA, sponge 2 and target
genes
- 5 miRNA, sponge 3 and target
genes
- 6 miRNA, sponge 4 and target
genes
- 7 miRNA, sponge 5 and target
genes
- 8 miRNA, sponge 6 and target
genes
- 9 miRNA, sponge 7 and target
genes
- 10 miRNA, sponge 8 and target
genes
- 11 miRNA, sponge 9 and target
genes
- 12 miRNA, sponge 10 and target
genes
- 13 miRNA, sponge 11 and target
genes
- 14 miRNA, sponge 12 and target
genes
- 15 miRNA, sponge 13 and target
genes
- 16 miRNA, sponge 14 and target
genes
- 17 miRNA, sponge 15 and target
genes
- 18 miRNA, sponge 16 and target
genes
- 19 miRNA, sponge 17 and target
genes
- 20 miRNA, sponge 18 and target
genes
- 21 miRNA, sponge 19 and no target
genes
- 22 miRNA, sponge 20 and target
genes
- 23 miRNA, sponge 21 and target
genes
- 24 miRNA, sponge 22 and target
genes
- 25 miRNA, sponge 23 and target
genes
- 26 miRNA, sponge 24 and target
genes
- 27
Session Info
Setup
suppressPackageStartupMessages({
(library(data.table))
(library(here))
(library(tidyverse))
(library(RColorBrewer))
(library(reshape2))
})
## [1] "reshape2" "RColorBrewer" "forcats" "stringr" "dplyr"
## [6] "purrr" "readr" "tidyr" "tibble" "ggplot2"
## [11] "tidyverse" "here" "data.table" "stats" "graphics"
## [16] "grDevices" "utils" "datasets" "methods" "base"
suppressMessages(source(here("src/R/plotEigengene.R")))
Load dataset and
samples
load(here("data/analysis/seidr/network.rda"))
samples <- read_csv(here("doc/samples_B2.csv"))
## Rows: 24 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (5): ScilifeID, SubmittedID, Stages, Description, ID
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
miRNA, sponge 1 and
target genes
plotEigengene(dat, "miRNA_12146-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_12146-5p")

plotEigengene(dat, "TRINITY_DN49527_c0_g1_i1",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN49527_c0_g1_i1")

plotEigengene(dat, "MA_10428924g0020",rep("bla", nrow(dat)),samples$Stages,title="MA_10428924g0020")

miRNA, sponge 2 and
target genes
plotEigengene(dat, "miRNA_12146-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_12146-5p")

plotEigengene(dat, "TRINITY_DN10084_c0_g5_i1",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN10084_c0_g5_i1")

plotEigengene(dat, "MA_10428924g0020",rep("bla", nrow(dat)),samples$Stages,title="MA_10428924g0020")

miRNA, sponge 3 and
target genes
plotEigengene(dat, "miRNA_12146-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_12146-5p")

plotEigengene(dat, "TRINITY_DN64598_c0_g1_i3",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN64598_c0_g1_i3")

plotEigengene(dat, "MA_10428924g0020",rep("bla", nrow(dat)),samples$Stages,title="MA_10428924g0020")

miRNA, sponge 4 and
target genes
plotEigengene(dat, "miRNA_12146-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_12146-5p")

plotEigengene(dat, "TRINITY_DN14989_c0_g3_i1",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN14989_c0_g3_i1")

plotEigengene(dat, "MA_10428924g0020",rep("bla", nrow(dat)),samples$Stages,title="MA_10428924g0020")

miRNA, sponge 5 and
target genes
plotEigengene(dat, "miRNA_1613-3p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_1613-3p")

plotEigengene(dat, "TRINITY_DN11832_c0_g1_i5",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN11832_c0_g1_i5")

plotEigengene(dat, "MA_945672g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_945672g0010")

plotEigengene(dat, "MA_488753g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_488753g0010")

plotEigengene(dat, "MA_127386g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_127386g0010")

plotEigengene(dat, "MA_505857g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_505857g0010")

plotEigengene(dat, "MA_10428475g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10428475g0010")

miRNA, sponge 6 and
target genes
plotEigengene(dat, "miRNA_1613-3p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_1613-3p")

plotEigengene(dat, "TRINITY_DN11832_c0_g1_i7",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN11832_c0_g1_i7")

plotEigengene(dat, "MA_945672g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_945672g0010")

plotEigengene(dat, "MA_488753g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_488753g0010")

plotEigengene(dat, "MA_127386g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_127386g0010")

plotEigengene(dat, "MA_505857g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_505857g0010")

plotEigengene(dat, "MA_10428475g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10428475g0010")

miRNA, sponge 7 and
target genes
plotEigengene(dat, "miRNA_1613-3p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_1613-3p")

plotEigengene(dat, "TRINITY_DN11832_c0_g1_i2",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN11832_c0_g1_i2")

plotEigengene(dat, "MA_945672g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_945672g0010")

plotEigengene(dat, "MA_488753g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_488753g0010")

plotEigengene(dat, "MA_127386g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_127386g0010")

plotEigengene(dat, "MA_505857g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_505857g0010")

plotEigengene(dat, "MA_10428475g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10428475g0010")

miRNA, sponge 8 and
target genes
plotEigengene(dat, "miRNA_1613-3p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_1613-3p")

plotEigengene(dat, "TRINITY_DN7435_c0_g1_i7",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN7435_c0_g1_i7")

plotEigengene(dat, "MA_945672g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_945672g0010")

plotEigengene(dat, "MA_488753g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_488753g0010")

plotEigengene(dat, "MA_127386g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_127386g0010")

plotEigengene(dat, "MA_505857g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_505857g0010")

plotEigengene(dat, "MA_10428475g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10428475g0010")

miRNA, sponge 9 and
target genes
plotEigengene(dat, "miRNA_203-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_203-5p")

plotEigengene(dat, "TRINITY_DN56799_c0_g1_i1",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN56799_c0_g1_i1")

plotEigengene(dat, "MA_10432357g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10432357g0010")

plotEigengene(dat, "MA_10433485g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10433485g0010")

plotEigengene(dat, "MA_10702g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10702g0010")

plotEigengene(dat, "MA_10426674g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10426674g0010")

plotEigengene(dat, "MA_11005g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_11005g0010")

miRNA, sponge 10 and
target genes
plotEigengene(dat, "miRNA_203-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_203-5p")

plotEigengene(dat, "TRINITY_DN64598_c0_g1_i3",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN64598_c0_g1_i3")

plotEigengene(dat, "MA_10432357g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10432357g0010")

plotEigengene(dat, "MA_10433485g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10433485g0010")

plotEigengene(dat, "MA_10702g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10702g0010")

plotEigengene(dat, "MA_10426674g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10426674g0010")

plotEigengene(dat, "MA_11005g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_11005g0010")

miRNA, sponge 11 and
target genes
plotEigengene(dat, "miRNA_25425-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_25425-5p")

plotEigengene(dat, "TRINITY_DN22441_c0_g1_i1",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN22441_c0_g1_i1")

plotEigengene(dat, "MA_10437032g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10437032g0010")

plotEigengene(dat, "MA_985g0020",rep("bla", nrow(dat)),samples$Stages,title="MA_985g0020")

plotEigengene(dat, "MA_913482g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_913482g0010")

plotEigengene(dat, "MA_10433629g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10433629g0010")

plotEigengene(dat, "MA_9198405g0020",rep("bla", nrow(dat)),samples$Stages,title="MA_9198405g0020")

miRNA, sponge 12 and
target genes
plotEigengene(dat, "miRNA_28675-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_28675-5p")

plotEigengene(dat, "TRINITY_DN22441_c0_g1_i1",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN22441_c0_g1_i1")

plotEigengene(dat, "MA_10437032g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10437032g0010")

plotEigengene(dat, "MA_985g0020",rep("bla", nrow(dat)),samples$Stages,title="MA_985g0020")

plotEigengene(dat, "MA_913482g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_913482g0010")

plotEigengene(dat, "MA_10433629g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10433629g0010")

plotEigengene(dat, "MA_9198405g0020",rep("bla", nrow(dat)),samples$Stages,title="MA_9198405g0020")

miRNA, sponge 13 and
target genes
plotEigengene(dat, "miRNA_29263-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_29263-5p")

plotEigengene(dat, "TRINITY_DN22441_c0_g1_i1",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN22441_c0_g1_i1")

plotEigengene(dat, "MA_10437032g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10437032g0010")

plotEigengene(dat, "MA_985g0020",rep("bla", nrow(dat)),samples$Stages,title="MA_985g0020")

plotEigengene(dat, "MA_913482g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_913482g0010")

plotEigengene(dat, "MA_10433629g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10433629g0010")

plotEigengene(dat, "MA_9198405g0020",rep("bla", nrow(dat)),samples$Stages,title="MA_9198405g0020")

miRNA, sponge 14 and
target genes
plotEigengene(dat, "miRNA_2964-3p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_2964-3p")

plotEigengene(dat, "TRINITY_DN52354_c0_g1_i4",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN52354_c0_g1_i4")

plotEigengene(dat, "MA_11619g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_11619g0010")

plotEigengene(dat, "MA_10429662g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10429662g0010")

miRNA, sponge 15 and
target genes
plotEigengene(dat, "miRNA_31183-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_31183-5p")

plotEigengene(dat, "TRINITY_DN19947_c0_g1_i2",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN19947_c0_g1_i2")

plotEigengene(dat, "MA_205171g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_205171g0010")

plotEigengene(dat, "MA_10434752g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10434752g0010")

miRNA, sponge 16 and
target genes
plotEigengene(dat, "miRNA_31183-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_31183-5p")

plotEigengene(dat, "TRINITY_DN11757_c0_g2_i2",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN11757_c0_g2_i2")

plotEigengene(dat, "MA_205171g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_205171g0010")

plotEigengene(dat, "MA_10434752g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10434752g0010")

miRNA, sponge 17 and
target genes
plotEigengene(dat, "miRNA_31183-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_31183-5p")

plotEigengene(dat, "TRINITY_DN11757_c0_g2_i3",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN11757_c0_g2_i3")

plotEigengene(dat, "MA_205171g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_205171g0010")

plotEigengene(dat, "MA_10434752g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10434752g0010")

miRNA, sponge 18 and
target genes
plotEigengene(dat, "miRNA_32209-3p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_32209-3p")

plotEigengene(dat, "TRINITY_DN9567_c0_g1_i4",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN9567_c0_g1_i4")

plotEigengene(dat, "MA_9061214g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_9061214g0010")

plotEigengene(dat, "MA_10431711g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10431711g0010")

plotEigengene(dat, "MA_820g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_820g0010")

plotEigengene(dat, "MA_39627g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_39627g0010")

miRNA, sponge 19 and
no target genes
plotEigengene(dat, "miRNA_3489-3p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_3489-3p")

plotEigengene(dat, "TRINITY_DN20880_c0_g1_i1",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN20880_c0_g1_i1")

miRNA, sponge 20 and
target genes
plotEigengene(dat, "miRNA_36092-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_36092-5p")

plotEigengene(dat, "TRINITY_DN13269_c0_g1_i4",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN13269_c0_g1_i4")

plotEigengene(dat, "MA_323184g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_323184g0010")

plotEigengene(dat, "MA_264506g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_264506g0010")

plotEigengene(dat, "MA_13307g0020",rep("bla", nrow(dat)),samples$Stages,title="MA_13307g0020")

plotEigengene(dat, "MA_80318g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_80318g0010")

plotEigengene(dat, "MA_10436921g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10436921g0010")

miRNA, sponge 21 and
target genes
plotEigengene(dat, "miRNA_36730-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_36730-5p")

plotEigengene(dat, "TRINITY_DN14121_c0_g1_i2",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN14121_c0_g1_i2")

plotEigengene(dat, "MA_35900g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_35900g0010")

miRNA, sponge 22 and
target genes
plotEigengene(dat, "miRNA_5305-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_5305-5p")

plotEigengene(dat, "TRINITY_DN1187_c0_g1_i7",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN1187_c0_g1_i7")

plotEigengene(dat, "MA_10435426g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10435426g0010")

plotEigengene(dat, "MA_10427079g0030",rep("bla", nrow(dat)),samples$Stages,title="MA_10427079g0030")

plotEigengene(dat, "MA_10434973g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10434973g0010")

plotEigengene(dat, "MA_9486006g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_9486006g0010")

plotEigengene(dat, "MA_81888g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_81888g0010")

plotEigengene(dat, "MA_10428192g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10428192g0010")

plotEigengene(dat, "MA_10090939g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10090939g0010")

plotEigengene(dat, "MA_639470g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_639470g0010")

plotEigengene(dat, "MA_251653g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_251653g0010")

plotEigengene(dat, "MA_205171g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_205171g0010")

plotEigengene(dat, "MA_9881339g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_9881339g0010")

plotEigengene(dat, "MA_10430890g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10430890g0010")

plotEigengene(dat, "MA_637235g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_637235g0010")

plotEigengene(dat, "MA_8729g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_8729g0010")

plotEigengene(dat, "MA_10426931g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10426931g0010")

miRNA, sponge 23 and
target genes
plotEigengene(dat, "miRNA_5305-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_5305-5p")

plotEigengene(dat, "TRINITY_DN1187_c0_g1_i12",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN1187_c0_g1_i12")

plotEigengene(dat, "MA_10435426g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10435426g0010")

plotEigengene(dat, "MA_10427079g0030",rep("bla", nrow(dat)),samples$Stages,title="MA_10427079g0030")

plotEigengene(dat, "MA_10434973g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10434973g0010")

plotEigengene(dat, "MA_9486006g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_9486006g0010")

plotEigengene(dat, "MA_81888g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_81888g0010")

plotEigengene(dat, "MA_10428192g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10428192g0010")

plotEigengene(dat, "MA_10090939g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10090939g0010")

plotEigengene(dat, "MA_639470g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_639470g0010")

plotEigengene(dat, "MA_251653g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_251653g0010")

plotEigengene(dat, "MA_205171g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_205171g0010")

plotEigengene(dat, "MA_9881339g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_9881339g0010")

plotEigengene(dat, "MA_10430890g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10430890g0010")

plotEigengene(dat, "MA_637235g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_637235g0010")

plotEigengene(dat, "MA_8729g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_8729g0010")

plotEigengene(dat, "MA_10426931g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10426931g0010")

miRNA, sponge 24 and
target genes
plotEigengene(dat, "miRNA_5305-5p",rep("bla", nrow(dat)),samples$Stages,title="miRNA_5305-5p")

plotEigengene(dat, "TRINITY_DN12482_c0_g1_i3",rep("bla", nrow(dat)),samples$Stages,title="TRINITY_DN12482_c0_g1_i3")

plotEigengene(dat, "MA_10435426g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10435426g0010")

plotEigengene(dat, "MA_10427079g0030",rep("bla", nrow(dat)),samples$Stages,title="MA_10427079g0030")

plotEigengene(dat, "MA_10434973g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10434973g0010")

plotEigengene(dat, "MA_9486006g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_9486006g0010")

plotEigengene(dat, "MA_81888g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_81888g0010")

plotEigengene(dat, "MA_10428192g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10428192g0010")

plotEigengene(dat, "MA_10090939g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10090939g0010")

plotEigengene(dat, "MA_639470g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_639470g0010")

plotEigengene(dat, "MA_251653g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_251653g0010")

plotEigengene(dat, "MA_205171g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_205171g0010")

plotEigengene(dat, "MA_9881339g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_9881339g0010")

plotEigengene(dat, "MA_10430890g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10430890g0010")

plotEigengene(dat, "MA_637235g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_637235g0010")

plotEigengene(dat, "MA_8729g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_8729g0010")

plotEigengene(dat, "MA_10426931g0010",rep("bla", nrow(dat)),samples$Stages,title="MA_10426931g0010")

Session Info
## R version 4.1.3 (2022-03-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.6 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] reshape2_1.4.4 RColorBrewer_1.1-3 forcats_0.5.1 stringr_1.4.0
## [5] dplyr_1.0.8 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0
## [9] tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1 here_1.0.1
## [13] data.table_1.14.2
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.8 lubridate_1.8.0 assertthat_0.2.1 rprojroot_2.0.3
## [5] digest_0.6.29 utf8_1.2.2 R6_2.5.1 cellranger_1.1.0
## [9] plyr_1.8.6 backports_1.4.1 reprex_2.0.1 evaluate_0.15
## [13] httr_1.4.2 highr_0.9 pillar_1.7.0 rlang_1.0.0
## [17] readxl_1.4.0 rstudioapi_0.13 jquerylib_0.1.4 rmarkdown_2.13
## [21] labeling_0.4.2 bit_4.0.4 munsell_0.5.0 broom_0.8.0
## [25] compiler_4.1.2 modelr_0.1.8 xfun_0.29 pkgconfig_2.0.3
## [29] htmltools_0.5.2 tidyselect_1.1.1 fansi_1.0.2 crayon_1.5.1
## [33] tzdb_0.3.0 dbplyr_2.1.1 withr_2.5.0 grid_4.1.2
## [37] jsonlite_1.7.3 gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2
## [41] magrittr_2.0.2 scales_1.2.0 vroom_1.5.7 cli_3.2.0
## [45] stringi_1.7.6 farver_2.1.0 fs_1.5.2 xml2_1.3.3
## [49] bslib_0.3.1 ellipsis_0.3.2 generics_0.1.2 vctrs_0.3.8
## [53] tools_4.1.2 bit64_4.0.5 glue_1.6.1 hms_1.1.1
## [57] parallel_4.1.2 fastmap_1.1.0 yaml_2.3.5 colorspace_2.0-3
## [61] rvest_1.0.2 knitr_1.38 haven_2.5.0 sass_0.4.1